3G0G

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinone inhibitor 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV.

Zhang, Z.Wallace, M.B.Feng, J.Stafford, J.A.Skene, R.J.Shi, L.Lee, B.Aertgeerts, K.Jennings, A.Xu, R.Kassel, D.B.Kaldor, S.W.Navre, M.Webb, D.R.Gwaltney, S.L.

(2011) J.Med.Chem. 54: 510-524

  • DOI: 10.1021/jm101016w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery of two classes of heterocyclic dipeptidyl peptidase IV (DPP-4) inhibitors, pyrimidinones and pyrimidinediones, is described. After a single oral dose, these potent, selective, and noncovalent inhibitors provide sustained reduction of pl ...

    The discovery of two classes of heterocyclic dipeptidyl peptidase IV (DPP-4) inhibitors, pyrimidinones and pyrimidinediones, is described. After a single oral dose, these potent, selective, and noncovalent inhibitors provide sustained reduction of plasma DPP-4 activity and lowering of blood glucose in animal models of diabetes. Compounds 13a, 27b, and 27j were selected for development.


    Organizational Affiliation

    Takeda San Diego, Inc., 10410 Science Center Drive, San Diego, California 92121, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B, C, D
740Homo sapiensMutation(s): 0 
Gene Names: DPP4 (ADCP2, CD26)
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to Gene View: DPP4
Go to UniProtKB:  P27487
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RUM
Query on RUM

Download SDF File 
Download CCD File 
A, B, C, D
2-({2-[(3R)-3-aminopiperidin-1-yl]-5-bromo-6-oxopyrimidin-1(6H)-yl}methyl)benzonitrile
C17 H18 Br N5 O
GGCILSXUAHLDMF-CQSZACIVSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RUMIC50: 5 nM (100) BINDINGDB
RUMIC50: 5 nM BINDINGMOAD
RUMIC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 122.906α = 90.00
b = 122.921β = 114.77
c = 145.092γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
PHASERphasing
DENZOdata reduction
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Advisory, Refinement description